Literature DB >> 15574958

Reevaluation and reduction of a PCR bias caused by reannealing of templates.

Shinya Kurata1, Takahiro Kanagawa, Yukio Magariyama, Kyoko Takatsu, Kazutaka Yamada, Toyokazu Yokomaku, Yoichi Kamagata.   

Abstract

We reevaluated the bias toward a 1:1 ratio of products in multitemplate PCR used in ecological studies and showed that the template reannealing at the annealing step would not cause the bias; however, the preferential homoduplex formation during temperature decrease from denaturation to annealing step would cause the bias.

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Year:  2004        PMID： 15574958      PMCID： PMC535213          DOI： 10.1128/AEM.70.12.7545-7549.2004

Source DB:  PubMed          Journal:  Appl Environ Microbiol        ISSN： 0099-2240            Impact factor:   4.792


  22 in total

1.  Microvariation artifacts introduced by PCR and cloning of closely related 16S rRNA gene sequences.

Authors:  A G Speksnijder; G A Kowalchuk; S De Jong; E Kline; J R Stephen; H J Laanbroek
Journal:  Appl Environ Microbiol       Date:  2001-01       Impact factor: 4.792

2.  Fluorescent quenching-based quantitative detection of specific DNA/RNA using a BODIPY((R)) FL-labeled probe or primer.

Authors:  S Kurata; T Kanagawa; K Yamada; M Torimura; T Yokomaku; Y Kamagata; R Kurane
Journal:  Nucleic Acids Res       Date:  2001-03-15       Impact factor: 16.971

3.  Bias and artifacts in multitemplate polymerase chain reactions (PCR).

Authors:  Takahiro Kanagawa
Journal:  J Biosci Bioeng       Date:  2003       Impact factor: 2.894

4.  Template-switching during DNA synthesis by Thermus aquaticus DNA polymerase I.

Authors:  S J Odelberg; R B Weiss; A Hata; R White
Journal:  Nucleic Acids Res       Date:  1995-06-11       Impact factor: 16.971

5.  Bias in template-to-product ratios in multitemplate PCR.

Authors:  M F Polz; C M Cavanaugh
Journal:  Appl Environ Microbiol       Date:  1998-10       Impact factor: 4.792

6.  DNA rehybridization during PCR: the 'Cot effect' and its consequences.

Authors:  F Mathieu-Daudé; J Welsh; T Vogt; M McClelland
Journal:  Nucleic Acids Res       Date:  1996-06-01       Impact factor: 16.971

7.  Effect of PCR template concentration on the composition and distribution of total community 16S rDNA clone libraries.

Authors:  D P Chandler; J K Fredrickson; F J Brockman
Journal:  Mol Ecol       Date:  1997-05       Impact factor: 6.185

8.  Evaluation of PCR-generated chimeras, mutations, and heteroduplexes with 16S rRNA gene-based cloning.

Authors:  X Qiu; L Wu; H Huang; P E McDonel; A V Palumbo; J M Tiedje; J Zhou
Journal:  Appl Environ Microbiol       Date:  2001-02       Impact factor: 4.792

9.  Hybrid DNA artifact from PCR of closely related target sequences.

Authors:  A R Shuldiner; A Nirula; J Roth
Journal:  Nucleic Acids Res       Date:  1989-06-12       Impact factor: 16.971

10.  Formation of chimeric DNA primer extension products by template switching onto an annealed downstream oligonucleotide.

Authors:  R Patel; M Lin; M Laney; N Kurn; S Rose; E F Ullman
Journal:  Proc Natl Acad Sci U S A       Date:  1996-04-02       Impact factor: 11.205
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  24 in total

1.  Bacterial community composition in Lake Tanganyika: vertical and horizontal heterogeneity.

Authors:  Aaike De Wever; Koenraad Muylaert; Katleen Van der Gucht; Samuel Pirlot; Christine Cocquyt; Jean-Pierre Descy; Pierre-Denis Plisnier; Wim Vyverman
Journal:  Appl Environ Microbiol       Date:  2005-09       Impact factor: 4.792

2.  PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample.

Authors:  Silvia G Acinas; Ramahi Sarma-Rupavtarm; Vanja Klepac-Ceraj; Martin F Polz
Journal:  Appl Environ Microbiol       Date:  2005-12       Impact factor: 4.792

3.  Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation.

Authors:  Eoin L Brodie; Todd Z Desantis; Dominique C Joyner; Seung M Baek; Joern T Larsen; Gary L Andersen; Terry C Hazen; Paul M Richardson; Donald J Herman; Tetsu K Tokunaga; Jiamin M Wan; Mary K Firestone
Journal:  Appl Environ Microbiol       Date:  2006-09       Impact factor: 4.792

4.  Rapid phylogenetic dissection of prokaryotic community structure in tidal flat using pyrosequencing.

Authors:  Bong-Soo Kim; Byung Kwon Kim; Jae-Hak Lee; Myungjin Kim; Young Woon Lim; Jongsik Chun
Journal:  J Microbiol       Date:  2008-08-31       Impact factor: 3.422

5.  Soil microbial community successional patterns during forest ecosystem restoration.

Authors:  Natasha C Banning; Deirdre B Gleeson; Andrew H Grigg; Carl D Grant; Gary L Andersen; Eoin L Brodie; D V Murphy
Journal:  Appl Environ Microbiol       Date:  2011-07-01       Impact factor: 4.792

6.  Mathematical modeling of 16S ribosomal DNA amplification reveals optimal conditions for the interrogation of complex microbial communities with phylogenetic microarrays.

Authors:  Oleg Paliy; Brent D Foy
Journal:  Bioinformatics       Date:  2011-06-07       Impact factor: 6.937

7.  Improved pipeline for reducing erroneous identification by 16S rRNA sequences using the Illumina MiSeq platform.

Authors:  Yoon-Seong Jeon; Sang-Cheol Park; Jeongmin Lim; Jongsik Chun; Bong-Soo Kim
Journal:  J Microbiol       Date:  2015-01-04       Impact factor: 3.422

8.  The Use of Degenerate Primers in qPCR Analysis of Functional Genes Can Cause Dramatic Quantification Bias as Revealed by Investigation of nifH Primer Performance.

Authors:  John Christian Gaby; Daniel H Buckley
Journal:  Microb Ecol       Date:  2017-04-07       Impact factor: 4.552

9.  Optimizing the analysis of human intestinal microbiota with phylogenetic microarray.

Authors:  Laura Rigsbee; Richard Agans; Brent D Foy; Oleg Paliy
Journal:  FEMS Microbiol Ecol       Date:  2010-12-13       Impact factor: 4.194

10.  Description of an unusual Neisseria meningitidis isolate containing and expressing Neisseria gonorrhoeae-Specific 16S rRNA gene sequences.

Authors:  Marion Walcher; Rhonda Skvoretz; Megan Montgomery-Fullerton; Vivian Jonas; Steve Brentano
Journal:  J Clin Microbiol       Date:  2013-07-17       Impact factor: 5.948
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